# Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models

## Documentation for package ‘momentuHMM’ version 1.4.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

AIC.momentuHMM | AIC
AICweights | Calculate Akaike information criterion model weights
allProbs | Matrix of all probabilities
checkPar0 | Check parameter length and order for a 'fitHMM' (or 'MIfitHMM') model
CIbeta | Confidence intervals for working (i.e., beta) parameters
circAngles | Convert standard direction angles (in radians relative to the x-axis) to turning angle covariates suitable for circular-circular regression on the angle mean
CIreal | Confidence intervals for the natural (i.e., real) parameters
crawlMerge | Merge crwData object with additional data streams and/or covariates
crawlWrap | Fit and predict tracks for using crawl
crwData | Constructor of 'crwData' objects
crwSim | Constructor of 'crwSim' objects
dbern_rcpp | Bernoulli density function
dbeta_rcpp | Probability density function of the beta distribution (written in C++)
dexp_rcpp | Exponential density function
dgamma_rcpp | Gamma density function
distAngle | Calculate distance between points y and z and turning angle between points x, y, and z
dlnorm_rcpp | Log-normal density function
dnorm_rcpp | Normal density function
dpois_rcpp | Poisson density function
dvm_rcpp | Von Mises density function
dweibull_rcpp | Weibull density function
dwrpcauchy_rcpp | Wrapped Cauchy density function
example | Example dataset
exGen | Example data simulation
expandPar | Expand vector of free working parameters to vector of all working parameters including any fixed parameters (used in fitHMM.R and nLogLike.R)
fitHMM | Fit a multivariate HMM to the data
forest | Example dataset
getCovNames | Get names of any covariates used in probability distribution parameters
getDM_rcpp | Get design matrix
getPar | Get starting values from momentuHMM, miHMM, or miSum object returned by fitHMM, MIfitHMM, or MIpool
getPar0 | Get starting values for new model from existing 'momentuHMM' model fit
getParDM | Get starting values on working scale based on design matrix and other parameter constraints
HMMfits | Constructor of 'HMMfits' objects
is.crwData | Is crwData
is.crwSim | Is crwSim
is.HMMfits | Is HMMfits
is.miHMM | Is miHMM
is.miSum | Is miSum
is.momentuHMM | Is momentuHMM
is.momentuHMMData | Is momentuHMMData
logAlpha | Forward log-probabilities
logBeta | Backward log-probabilities
miExample | Example dataset
MIfitHMM | Fit HMMs to multiple imputation data
miHMM | Constructor of 'miHMM' objects
MIpool | Calculate pooled parameter estimates and states across multiple imputations
miSum | Constructor of 'miSum' objects
momentuHMM | Constructor of 'momentuHMM' objects
momentuHMMData | Constructor of 'momentuHMMData' objects
n2w | Scaling function: natural to working parameters.
nLogLike | Negative log-likelihood function
nLogLike_rcpp | Negative log-likelihood
parDef | Parameters definition
plot.crwData | Plot 'crwData'
plot.miHMM | Plot 'miHMM'
plot.miSum | Plot 'miSum'
plot.momentuHMM | Plot 'momentuHMM'
plot.momentuHMMData | Plot 'momentuHMMData'
plotPR | Plot pseudo-residuals
plotSat | Plot observations on satellite image
plotSpatialCov | Plot observations on raster image
plotStates | Plot states
plotStationary | Plot stationary state probabilities
prepData | Preprocessing of the data streams and covariates
print.miHMM | Print 'miHMM'
print.miSum | Print 'miSum'
print.momentuHMM | Print 'momentuHMM'
pseudoRes | Pseudo-residuals
setModelName | Set 'modelName' for a 'momentuHMM', 'miHMM', 'HMMfits', or 'miSum' object
setStateNames | Set 'stateNames' for a 'momentuHMM', 'miHMM', 'HMMfits', or 'miSum' object
simData | Simulation tool
simObsData | Observation error simulation tool
stateProbs | State probabilities
stationary | Stationary state probabilities
summary.momentuHMMData | Summary 'momentuHMMData'
timeInStates | Calculate proportion of time steps assigned to each state (i.e. "activity budgets")
timeInStates.HMMfits | Calculate proportion of time steps assigned to each state (i.e. "activity budgets")
timeInStates.miHMM | Calculate proportion of time steps assigned to each state (i.e. "activity budgets")
timeInStates.momentuHMM | Calculate proportion of time steps assigned to each state (i.e. "activity budgets")
trMatrix_rcpp | Transition probability matrix
turnAngle | Turning angle
viterbi | Viterbi algorithm
w2n | Scaling function: working to natural parameters
XBloop_rcpp | Get XB